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Antibody Research & Epitope Mapping

Pinpoint exactly where your antibody binds at single amino acid resolution. Validate specificity, characterize cross-reactivity, and define critical residues with high-densitiy peptide microarrays.
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What peptide microarrays enable

Know where your antibodies interact and how

Most antibody validation stops at “it binds”. Epitope mapping tells you where (which amino acids), why (critical residues), and how (conformational vs. linear). From off-target binding to epitope diversity, get the information you need to shape better candidates and avoid surprises downstream.

Table of Contents

Validate specificity & detect cross-reactivity

Confirm your antibody is doing exactly what you think it is. Find out early if it isn’t.

Screen thousands of peptides in one experiment

Simultaneously test up to 45,000 peptides coverning homologous proteins, related antigens, or even random motifs.

Understand what drives unexpected signals

Find out if sequence similarity is driving cross-reactivity, or if post-translational modifications alter specificity.

Compare multiple antibodies side by side

Profile mono- and polyclonal samples to understand epitope diversity across shared targets.

Map linear & conformational epitopes

Most peptide mapping platforms can only detect linear epitopes. Ours goes beyond.

Probe cyclic constrained peptides for conformational epitopes

Cyclic peptides in varying loop sizes make screening diverse epitope structures possible.

Map interactions in single amino acid resolution

Peptides that overlap with a single residue shift means every position can be examined.

Works with complex samples, not just prurified antibodies

Profile polyclonal sera or plasma to identify unique binding signatures across mixed antibody populations.

Identify critical residues & guide optimization

Knowing where an antibody binds is a start. Knowing why is what drives better antibodies.

Substitution scans identify required vs. variable amino acid positions

Systematically replace each position in the epitope to find out which interactions make or break binding.

Refine peptide binding affinities with residue-level data

Optimize peptide design for better targeted therapeutics or more sensitive diagnostics.

Strengthen intellectual property claims with detailed epitope information

Identify strongly binding or tolerated sequences for increased protection of IP claims.

Research questions answered

Specific answers to real research questions

The most useful way to think about epitope mapping results is in terms of what the data tells you. Here’s a look at some real projects we’ve taken on (with the actual readouts you can expect to get with our microarrays).

Specificity

How critical is phosphorylation to my antibody's binding?

Two anti-ubiquitin antibodies show different binding specificities: one only binding to phosphorylated motifs, and the other with preferential binding to unmodified ubiquitin peptides.
Cross-Reactivity

Is my antibody binding the right target?

We compared two commercial anti-TGM2 antibodies for target specificity and observed protein-level off-target binding for one of the two antibodies. Further epitope-level analysis on peptide microarrays revealed cross-reactivity to peptide sequences similar to the TGM2 target.
Read application note →
Binding Mode

Is recognition based on a linear or conformational epitope?

Comparison of microarray scans and intensity plots from mapping an anti-CD20 antibody against linear and cyclic constrained peptides. Clear epitope peaks on cyclic constrained peptides indicate a conformational epitope.
Read application note →
How it works

Antibody binding can be complex.
Epitope mapping shouldn't have to be.

A single experiment delivers a full amino acid-level profile of your sample's antibody binding activity.
Method comparison

Why map epitopes with PEPperPRINT

We know choosing the right method for your antibody analysis isn’t always dependent on a single factor. Our platform offers a balanced approach that combines high-resolution data with practical benefits for throughput, cost, and accessibility. Here’s how we compapre to traditional epitope mapping methods.

PEPperCHIP® Peptide Microarrays

Other peptide microarrays / peptide libraries

Shotgun mutagenesis / deep mutational scanning

Peptide / protein display

X-ray crystallography

HDX-MS / XL-MS
Linear epitopes ✓✓✓ ✓✓✓ ✓✓✓ ✓✓ ✓✓✓ ✓✓✓
Conformational epitopes ✓ ✓ ✓✓ ✕ ✓✓✓ ✓✓✓
Throughput rate ✓✓✓ ✓✓✓ ✓ ✓✓✓ ✕ ✓✓
Epitope resolution ✓✓✓ ✕ ✓✓ ✓ ✓✓✓ ✓
Costs € € € € € € € € € € € € € € €
Sample need Low Moderate High Low High High

Not sure which solution is best for you? We can help.

Start the conversation
PROJECT WORKFLOW

What a typical epitope mapping study looks like

Whether you run the assay in your own lab or leave it all to us, here’s what you can expect at every stage.

1

Target definition & library design

~1–2 days

PEPperPRINT

Design the microarray
We design the peptide library based on your target sequences and research objectives, then confirm the layout before production begins.

You

Define your question
Provide your research question and antigen sequence (FASTA or UniProt ID). We handle everything from here.
2

Microarray production

~5–6 weeks

PEPperPRINT

Synthesize & forward
We produce the microarray and run quality controls, then send them directly to our service labs.

You

Ship your sample
Send us your sample. We handle the rest.
3

Immunoassay

2 days

PEPperPRINT

Run the assay
We run the fluorescence-based immunoassay with your samples and scan the microarray to collect data.
View example scan output

You

Sit tight
Nothing required at this stage. If requested, we can send you the resulting scans at this point, though we usually send everything together with the report.
4

Data & analysis

~1-2 weeks

PEPperPRINT

Deliver your report
We analyze the scans data and deliver a full written report with annotated scans, intensity plots, and interpreted data.
View sample report

You

Receive your report
Your full analysis report is delivered digitally, ready to share with your team or include in a publication.
1

Target definition & library design

~1–2 days

PEPperPRINT

Design the microarray
We design the peptide library based on your target sequences and research objectives, then confirm the layout before production begins.

You

Define your question
Provide your research question and antigen sequence. Let us know if you’ll be needing additional accessories and reagents for running the assays.
2

Microarray production

~5–6 weeks

PEPperPRINT

Synthesize & ship
We produce the microarray and run quality controls. Then, we ship it to your facility.

You

Await delivery
Your microarray ships directly to your lab. Prepare your sample and reagents in the meantime.
3

Immunoassay

2 days

PEPperPRINT

Protocol support
We're on standby for protocol guidance and troubleshooting while you run the assay in your own lab.

You

Run the assay
Perform the immunoassay in your lab following our protocol. Contact us anytime for support.
4

Data & analysis

~1-2 weeks

PEPperPRINT

Analysis support
We're available for data interpretation support and can review your findings on request.

You

Analyse your data
Use our documentation and recommended analysis tools to interpret your results. We're on hand if you need us.
View example output
Related applications

Beyond epitope mapping

Antibody characterization rarely ends with the epitope. Here's what researchers typically explore next:

Vaccines & Therapeutic Immunogenicity Profiling

Profile immune responses for vaccine optimization, anti-drug antibody detection, and immunotherapy development across preclinical to clinical stages.
Explore application →

Cancer Immunology & Neoantigen Discovery

Characterize antibodies targeting tumor-associated antigens and validate binding specificity against clinical candidates.
Explore application →

Infectious Disease & Pathogen Profiling

Profile immune responses to viral and bacterial antigens for vaccine development, seroprevalence studies, and pathogen surveillance.
Explore application →

Find out exactly where your antibody binds

Every antibody project is different. Whether you're validating a research tool, characterizing a therapeutic candidate, or troubleshooting unexpected results, we'll help you design the right experiment.
Start the conversation
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Frequently Asked Questions

Before you get started

How does your epitope mapping work?
We use a peptide scanning approach using a fluorescence-based immunoassay. Basically, we "recreate" your target protein as overlapping peptides on a chip, incubate it with your sample, stain it with a secondary antibody, and identify the epitope/s by quantifying fluorescent signals of each peptide on the array.

First, we need the antigen sequence in FASTA format or the Uniprot ID. We will discuss with you how much serum or purified antibody you’ll need to run the assays for your specific project.

The exact amount depends on the experimental design, but for standard mapping projects, we typically work with 5–20 µg purified antibody or 10–40 µL serum or plasma.
Yes, in this case we can skip directly to substitution scans. Like an alanine scan, except instead of just replacing each amino acid position with alanine, we replace each amino acid with every other amino acid (or D-amino acids on request) and evaluate how each peptide variant binds compared to the original epitope.
We can. In addition to target screening and antibody validation, you can also outsource antibody isolation to us. Once we know the epitope, we can move on to our validated column-based approach to isolate your target antibodies from polyclonal samples.

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